Microvirus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1057724 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Viral metagenome in feces from piglets with diarrhea
| PRJNA473026 | ENA
Project description:Backgroud:Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or the abnormality of the cloned animals, but the underlying mechanism of the abnormal phenotype in the cloned piglets remains unrevealed. Some cloned piglets in our study showed abnormal phenotypes such as big tongue (longer and thicker), limp, and exomphalos, which is similar to the human BWS syndrome. Here we conducted DNA methylation (DNAm) immunoprecipitation binding high throughput sequencing (MeDIP-seq) and RNA sequencing (RNA-seq) of muscle tissues of cloned piglets to investigate the relationship of abnormal DNAm with gene dysregulation and the unusual phenotypes in cloned piglets. Results:Analysis of the methylomes revealed that abnormal cloned piglets suffered more hypomethylated differentially methylated regions (DMRs) than hypermethylated DMRs compared to the normal cloned piglets. The DNAm level in the CpG Island was higher in the abnormal cloned piglets. Some repetitive elements, such as SINE/tRNA-Glu Satellite/centr also showed significant differences. Besides we detected 1,711 differentially expressed genes (DEGs) between the two groups, of which 243 genes also changed methylation level in the abnormal cloned piglets. The altered DNA methylation mainly affected the low and silent expression genes. We also found some interesting pathways and genes, such as MAPK signalling pathway, hypertrophic cardiomyopathy pathway, TPM3 gene and the imprinted gene PLAGL1, which may played important roles in the abnormal phenotype development. Conclusions;The abnormal cloned piglets showed substantial change both in the DNAm and the gene expression levels. Our data may provide new insights into understanding the molecular mechanisms of the reprogramming of genetic information in cloned animals. We dissected the biceps femoris muscle from the abnormal cloned piglets and the normal cloned piglets, and analyzed the difference of MeDIP-seq and RNA-seq between the two groups.
2014-09-03 | E-GEOD-51476 | biostudies-arrayexpress
Project description:Sixty crossbred piglets (Duroc*Landrace*Yorkshire) weaned at the age of 21 days were maintained for one week and had free access to feed and water. During this week, all the piglets were scored for the severity of diarrhea. Diarrhea index was scored as follows: 1= hard feces; 2= no scours, feces of normal consistency; 3= mild scours, soft, partially formed feces; 4= moderate scours, loose, semi-liquid feces; 5= watery feces; as previously did Those piglets with a score of 4 or 5 for three continuous days were designated as diarrhea piglets, while those piglets with a score of 1 or 2 for three continuous days were designated as normal piglets..
2022-01-03 | GSE192690 | GEO
Project description:The objective is to study the relevance of porcine intestinal models (incl. piglet jejunums, 2D and 3D organoids derived from piglet jejunums and swine testicular cells) to study intestinal functions and to decipher the host-virus interactions during viral porcine coronavirus infection. This dataset includes RNA-seq profiling of 54 samples covering the four experimental models mentioned above, uninfected or infected with the Purdue P115 strain of the transmissible gastroenteritis virus (TGEV). Details about the experimental models: - For the in vivo model, jejunums of five week old piglets were extracted. - For the organoid model, first jejunum crypts of newborn piglets were extracted and profiled. Then, 3D organoids derived from these crypts were profiled after 5, 14 and 25 passages. Last, 2D organoids derived from 3D organoids at passage 25 were also included. - For the cellular model, we relied on swine testicular cells (ST cells) at passage 53. Samples were either mock-infected or infected with TGEV (Purdue P115 strain) at MOI 0.06 (ST cells), 0.06 and 1 (2D organoids), and 10^4.75 TCID50 (piglets). For ST cells and organoids, the total RNA was recovered at 9hpi (hours post-infection) and 24hpi. For piglets jejunums, only the latest time point was included (24hpi). For each model and each condition (control / infected), three replicates were performed.
2025-10-10 | E-MTAB-15113 | biostudies-arrayexpress
Project description:high throughput sequencing of the metagenome of mexican children
2020-03-16 | GSE143207 | GEO
Project description:Somatic cell nuclear transfer has brought considerable chances to breed excellent breeds and protect endanger animals, while also produced numerous fail embryos and abnormal individuals due to inefficient epigenetic modification at the same time. To understand some mechanisms of abnormal piglets with phenotypes such as macroglossia, standing and walking disabilities in our study and find some differences between abnormal piglets and conventionally bred normal piglets, DNA methylation profile and genome-wide gene expression were conducted in two groups, using methylated DNA immunoprecipitation binding highthroughput sequencing (MeDIP-Seq) and RNA sequencing(RNA-Seq). We generated and provided a genome-wide DNA methylation and gene expression profile for abnormal cloned and conventionally bred piglets. We detected a total of 1493 genes differentially expressed in two groups and 382 of these genes also differentially methylated in two groups. Analysis of relationship between DNA methylation and gene expression revealed that DNA methylation levels had significantly negative and monotonic correlation with gene expression levels in particular regions of genes while no obvious monotonic correlation in other regions. Besides, we found some interesting genes and pathways such as MYH7 and mTOR signalling pathway that may played essential role in muscle growth and development. Briefly, these results provide reliable data for future epigenetic studies and may help to uncover the mechanism of failure clones via SCNT. We dissected the leg muscle from the cloned piglets and the conventionally bred piglets, and analyzed the difference of MeDIP-seq and RNA-seq between the two groups. As for data of abnormal cloned piglets, we downloaded it from GEO under Super-Series accession No. GSE51477, including SubSeries accession No.GSE51282 for RNA-seq data (No. GSM1241829 for abnormal cloned group) and SubSeries accession No. GSE51476 for MeDIP-seq data (No. GSM1246252 for abnormal cloned group).
2016-02-26 | E-GEOD-70004 | biostudies-arrayexpress
Project description:Viral metagenome of swine serum: 26 serum with respiratory disease symptoms of piglets
| PRJNA390017 | ENA
Project description:MicroRNAs (miRNAs) in serum are very stable and specific. Moreover, serum miRNAs are non-destructive and convenient. Studies have shown that the changes of serum miRNAs are closely relative to the pathological stresses and diseases. Our previous studies suggested that weaning stress induced the abnormal miRNA transcriptome in the intestine of piglets. In this project, we will further screen serum miRNA expression in piglets induced by weaning stress using miRNA microarray. Microarrays containing 422 porcine unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between weaning piglets at 4 d after weaning and suckling piglets at the same days old. A total of 115 differentally expressed miRNAs were found,therein 63 miRNAs upregulated and 52 miRNA downregulated; 64 miRNAs are statistically significant but have low signals (signal < 500);122 miRNAs are not statistically significant (p > 0.01); the remaining 132 miRNAs have not detected signals.
2016-09-21 | GSE69920 | GEO